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This page was generated on 2024-07-18 11:41 -0400 (Thu, 18 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4683
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4379
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4450
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4399
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1917/2248HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SIAMCAT 2.9.0  (landing page)
Jakob Wirbel
Snapshot Date: 2024-07-17 14:00 -0400 (Wed, 17 Jul 2024)
git_url: https://git.bioconductor.org/packages/SIAMCAT
git_branch: devel
git_last_commit: 665aeef
git_last_commit_date: 2024-04-30 11:06:40 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for SIAMCAT on lconway

To the developers/maintainers of the SIAMCAT package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SIAMCAT.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: SIAMCAT
Version: 2.9.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SIAMCAT_2.9.0.tar.gz
StartedAt: 2024-07-18 00:17:10 -0400 (Thu, 18 Jul 2024)
EndedAt: 2024-07-18 00:22:37 -0400 (Thu, 18 Jul 2024)
EllapsedTime: 327.9 seconds
RetCode: 0
Status:   OK  
CheckDir: SIAMCAT.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SIAMCAT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SIAMCAT_2.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/SIAMCAT.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SIAMCAT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SIAMCAT’ version ‘2.9.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SIAMCAT’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    help      1.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
make.predictions          27.822  0.399  28.394
train.model               26.889  0.536  27.545
model.interpretation.plot 26.603  0.389  27.099
assign-model_list         26.098  0.503  26.722
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/SIAMCAT.Rcheck/00check.log’
for details.


Installation output

SIAMCAT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SIAMCAT
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘SIAMCAT’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SIAMCAT)

Tests output


Example timings

SIAMCAT.Rcheck/SIAMCAT-Ex.timings

nameusersystemelapsed
accessSlot0.0080.0040.012
add.meta.pred0.5620.0150.586
assign-associations0.0060.0010.008
assign-data_split0.0050.0010.006
assign-eval_data0.0080.0010.010
assign-filt_feat0.0070.0010.009
assign-label0.0080.0010.009
assign-meta0.0280.0010.030
assign-model_list26.098 0.50326.722
assign-norm_feat0.0090.0010.011
assign-orig_feat0.0130.0020.015
assign-physeq0.0080.0020.010
assign-pred_matrix0.0060.0020.008
assoc_param-methods0.0060.0020.008
association.plot0.2260.0160.244
associations-methods0.0260.0040.030
check.associations0.0120.0010.014
check.confounders0.4700.0230.497
create.data.split0.0230.0020.024
create.label0.0030.0020.004
data_split-methods0.0050.0020.007
eval_data-methods0.0060.0010.007
evaluate.predictions1.9410.0692.023
feature_type-methods0.0050.0020.007
feature_weights-methods0.0050.0020.007
filt_feat-methods0.0050.0010.007
filt_params-methods0.0060.0020.007
filter.features0.0380.0070.045
filter.label0.0080.0010.010
get.filt_feat.matrix0.0070.0020.010
get.norm_feat.matrix0.0070.0020.009
get.orig_feat.matrix0.0070.0020.009
label-methods0.0060.0020.007
make.predictions27.822 0.39928.394
meta-methods0.0230.0020.026
model.evaluation.plot0.0470.0080.058
model.interpretation.plot26.603 0.38927.099
model_list-methods0.0060.0020.008
model_type-methods0.0060.0020.007
models-methods0.0060.0020.008
norm_feat-methods0.0070.0020.008
norm_params-methods0.0070.0020.008
normalize.features0.0160.0010.018
orig_feat-methods0.0070.0020.009
physeq-methods0.0090.0010.010
pred_matrix-methods0.0050.0020.006
read.label0.0080.0020.009
read.lefse0.7470.0200.771
select.samples0.0680.0030.071
siamcat0.9500.0200.975
siamcat.to.lefse0.0200.0020.022
siamcat.to.maaslin0.0210.0020.023
summarize.features2.2280.2122.450
train.model26.889 0.53627.545
validate.data0.0220.0020.024
volcano.plot0.0120.0040.016
weight_matrix-methods0.0060.0010.007